Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome

@inproceedings{Stevenson2013SourcesOB,
  title={Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome},
  author={Kraig R Stevenson and Joseph D Coolon and Patricia J Wittkopp},
  booktitle={BMC Genomics},
  year={2013}
}
RNA-seq can be used to measure allele-specific expression (ASE) by assigning sequence reads to individual alleles; however, relative ASE is systematically biased when sequence reads are aligned to a single reference genome. Aligning sequence reads to both parental genomes can eliminate this bias, but this approach is not always practical, especially for non-model organisms. To improve accuracy of ASE measured using a single reference genome, we identified properties of differentiating sites… CONTINUE READING
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